Ruby-Helix: An implementation of helical image processing based on object-oriented scripting language

Metlagel, Zoltan; Kikkawa, Yuichiro; Kikkawa, Masahide

doi:10.1016/j.jsb.2006.07.015

Cited by 45 publications

(37 citation statements)

References 29 publications

(37 reference statements)

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“…The initial helical parameters were determined using the Brandeis Helical Package (19) to calculate the Bessel orders of the basic layer lines (6 and Ϫ6) ( Fig. 1A and B) and the Ruby-Helix package to estimate a repeat distance of 110 Å (20). These were later refined by IHRSR to a helical rise of 38 Å and a rotation between subunits of 22.4°.…”

Section: Methodsmentioning

confidence: 99%

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Bebeacua

Lai

Vegge

et al. 2013

J Virol

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c Tailed phages are genome delivery machines exhibiting unequaled efficiency acquired over more than 3 billion years of evolution. Siphophages from the P335 and 936 families infect the Gram-positive bacterium Lactococcus lactis using receptor-binding proteins anchored to the host adsorption apparatus (baseplate). Crystallographic and electron microscopy (EM) studies have shed light on the distinct adsorption strategies used by phages of these two families, suggesting that they might also rely on different infection mechanisms. Here, we report electron microscopy reconstructions of the whole phage TP901-1 (P335 species) and propose a composite EM model of this gigantic molecular machine. Our results suggest conservation of structural proteins among tailed phages and add to the growing body of evidence pointing to a common evolutionary origin for these virions. Finally, we propose that host adsorption apparatus architectures have evolved in correlation with the nature of the receptors used during infection.

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Section: Methodsmentioning

confidence: 99%

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Bebeacua

Lai

Vegge

et al. 2013

J Virol

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“…Image processing for subtomogram averaging was performed as described previously ) using the IMOD software package ( Kremer et al, 1996), custom Ruby-Helix scripts (Metlagel et al, 2007) and the PEET software suite (Nicastro et al, 2006). The effective resolutions were ∼4.9 nm (Fig.…”

Section: Image Processingmentioning

confidence: 99%

Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro

Oda

Abe

Yanagisawa

et al. 2016

Journal of Cell Science

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The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complex in vitro. Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler.

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“…Tomograms of intact axonemes with a high signal-to-noise ratio were selected and used for subtomogram averaging of the 96-nm repeats of the outer DMTs. Alignment and averaging of subtomograms were conducted using custom RubyHelix scripts (Metlagel et al, 2007) and the PEET (Particle Estimation for Electron Tomography) software suite (Nicastro et al, 2006). For subtomogram averaging of CP structures, we cut out the subvolumes of 220 × 220 × 220 pixels, including CP microtubules at the center of the volume, every 16 nm along the center of the axoneme.…”

Section: Image Processingmentioning

confidence: 99%

Mechanosignaling between central apparatus and radial spokes controls axonemal dynein activity

Oda¹,

Yanagisawa²,

Yagi³

et al. 2014

J Gen Physiol

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Ruby-Helix: An implementation of helical image processing based on object-oriented scripting language

Cited by 45 publications

References 29 publications

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Visualizing a Complete Siphoviridae Member by Single-Particle Electron Microscopy: the Structure of Lactococcal Phage TP901-1

Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro

Mechanosignaling between central apparatus and radial spokes controls axonemal dynein activity

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